Starting phenix.real_space_refine (version: dev)
on Thu May 12 19:08:37 2022 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/05_2022/6ww2_21927.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/05_2022/6ww2_21927.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/05_2022/6ww2_21927.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/05_2022/6ww2_21927.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/05_2022/6ww2_21927.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ww2_21927/05_2022/6ww2_21927.pdb"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib"
  Total number of atoms: 7594
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1682
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1682
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 211, 'PCIS': 2}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "K"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 921
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 1624
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1624
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 9, 'TRANS': 201, 'PCIS': 1}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "R"
      Number of atoms: 3367
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3367
          Classifications: {'peptide': 425}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 12, 'TRANS': 411, 'PCIS': 1}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 4.82, per 1000 atoms: 0.63
  Number of scatterers: 7594
  At special positions: 0
  Unit cell: (112.112, 146.608, 98.098, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1432      8.00
     N    1273      7.00
     C    4857      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.02
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 222 " - pdb=" SG  CYS R 298 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 315 " - pdb=" SG  CYS R 390 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.11
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 13 sheets defined
      38.8% alpha, 23.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'H' and resid 65 through 68
      removed outlier: 3.667A  pdb=" N   LYS H  68 " --> pdb=" O   ASP H  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 65 through 68'
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.945A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 107 through 112
      removed outlier: 3.659A  pdb=" N   TRP H 111 " --> pdb=" O   GLY H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 202 through 206
      removed outlier: 3.703A  pdb=" N   GLN H 206 " --> pdb=" O   LEU H 203 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 87 through 91
      removed outlier: 3.967A  pdb=" N   THR K  91 " --> pdb=" O   PRO K  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 94 through 98
      removed outlier: 3.735A  pdb=" N   LEU L  97 " --> pdb=" O   TYR L  94 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL L  98 " --> pdb=" O   TYR L  95 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 94 through 98'
    Processing helix  chain 'L' and resid 185 through 189
      removed outlier: 4.252A  pdb=" N   GLU L 189 " --> pdb=" O   LYS L 185 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 185 through 189'
    Processing helix  chain 'R' and resid 211 through 215
      removed outlier: 3.566A  pdb=" N   GLN R 214 " --> pdb=" O   ARG R 211 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL R 215 " --> pdb=" O   THR R 212 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 211 through 215'
    Processing helix  chain 'R' and resid 228 through 230
      No H-bonds generated for 'chain 'R' and resid 228 through 230'
    Processing helix  chain 'R' and resid 231 through 261
      removed outlier: 4.704A  pdb=" N   PHE R 237 " --> pdb=" O   THR R 233 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE R 239 " --> pdb=" O   ALA R 235 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   GLY R 240 " --> pdb=" O   THR R 236 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   TRP R 242 " --> pdb=" O   TRP R 238 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   LEU R 245 " --> pdb=" O   LEU R 241 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   THR R 250 " --> pdb=" O   CYS R 246 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR R 252 " --> pdb=" O   ILE R 248 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR R 253 " --> pdb=" O   SER R 249 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL R 254 " --> pdb=" O   THR R 250 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ALA R 255 " --> pdb=" O   SER R 251 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 267
      No H-bonds generated for 'chain 'R' and resid 265 through 267'
    Processing helix  chain 'R' and resid 268 through 292
      removed outlier: 4.188A  pdb=" N   ILE R 272 " --> pdb=" O   GLU R 268 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   PHE R 273 " --> pdb=" O   ARG R 269 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   TYR R 278 " --> pdb=" O   LEU R 274 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   LEU R 279 " --> pdb=" O   SER R 275 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   CYS R 280 " --> pdb=" O   ALA R 276 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE R 285 " --> pdb=" O   VAL R 281 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 292 through 297
      removed outlier: 3.679A  pdb=" N   VAL R 296 " --> pdb=" O   GLY R 292 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA R 297 " --> pdb=" O   HIS R 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 292 through 297'
    Processing helix  chain 'R' and resid 314 through 345
      removed outlier: 4.028A  pdb=" N   VAL R 318 " --> pdb=" O   LEU R 314 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 349 through 379
      removed outlier: 3.627A  pdb=" N   TYR R 356 " --> pdb=" O   ALA R 352 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   TYR R 359 " --> pdb=" O   GLY R 355 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   LEU R 362 " --> pdb=" O   GLN R 358 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TRP R 365 " --> pdb=" O   HIS R 361 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LEU R 366 " --> pdb=" O   LEU R 362 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ILE R 367 " --> pdb=" O   ALA R 363 " (cutoff:3.500A)
      Proline residue:  R 368  - end of helix
    Processing helix  chain 'R' and resid 396 through 404
    Processing helix  chain 'R' and resid 404 through 1025
      removed outlier: 3.831A  pdb=" N   LEU R 408 " --> pdb=" O   VAL R 404 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   VAL R 409 " --> pdb=" O   LEU R 405 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU R 412 " --> pdb=" O   LEU R 408 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   PHE R 418 " --> pdb=" O   VAL R 414 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ASN R1018 " --> pdb=" O   THR R1014 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1029 through 1049
      removed outlier: 4.204A  pdb=" N   LYS R1037 " --> pdb=" O   ASP R1033 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA R1048 " --> pdb=" O   ASP R1044 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1064 through 1086
      removed outlier: 4.640A  pdb=" N   PHE R1070 " --> pdb=" O   PHE R1066 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   LYS R1082 " --> pdb=" O   ASP R1078 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LEU R1083 " --> pdb=" O   ASP R1079 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA R1084 " --> pdb=" O   ALA R1080 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1089 through 1098
    Processing helix  chain 'R' and resid 1098 through 1106
      removed outlier: 4.523A  pdb=" N   THR R1102 " --> pdb=" O   GLN R1098 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TYR R1106 " --> pdb=" O   THR R1102 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 1106 through 479
      removed outlier: 3.804A  pdb=" N   ARG R1113 " --> pdb=" O   LYS R1109 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU R1118 " --> pdb=" O   ALA R1114 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU R 446 " --> pdb=" O   LYS R 442 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE R 448 " --> pdb=" O   GLU R 444 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   ARG R 449 " --> pdb=" O   LYS R 445 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   PHE R 453 " --> pdb=" O   ARG R 449 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   THR R 454 " --> pdb=" O   ILE R 450 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL R 459 " --> pdb=" O   LEU R 455 " (cutoff:3.500A)
      Proline residue:  R 460  - end of helix
      removed outlier: 3.919A  pdb=" N   HIS R 473 " --> pdb=" O   LEU R 469 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 500 through 511
      removed outlier: 3.805A  pdb=" N   LYS R 506 " --> pdb=" O   VAL R 502 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TYR R 507 " --> pdb=" O   LEU R 503 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   PHE R 508 " --> pdb=" O   MET R 504 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU R 511 " --> pdb=" O   TYR R 507 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 511 through 520
      removed outlier: 4.257A  pdb=" N   ILE R 515 " --> pdb=" O   LEU R 511 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR R 516 " --> pdb=" O   VAL R 512 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 523 through 536
      removed outlier: 4.233A  pdb=" N   ARG R 536 " --> pdb=" O   ARG R 532 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 13 through 15
      removed outlier: 3.705A  pdb=" N   ALA H  52 " --> pdb=" O   TRP H  39 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   ARG H  41 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   TRP H  50 " --> pdb=" O   ARG H  41 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   TYR H  53 " --> pdb=" O   SER H  62 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER H  62 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.068A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.068A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168
      removed outlier: 3.597A  pdb=" N   TYR H 208 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6
      removed outlier: 3.738A  pdb=" N   GLN K   3 " --> pdb=" O   SER K  25 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER K  25 " --> pdb=" O   GLN K   3 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   GLY K  16 " --> pdb=" O   SER K  85 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   SER K  85 " --> pdb=" O   GLY K  16 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 11 through 12
      removed outlier: 6.466A  pdb=" N   VAL K  12 " --> pdb=" O   GLN K 116 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   THR K 118 " --> pdb=" O   VAL K  12 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   VAL K 117 " --> pdb=" O   ALA K  92 " (cutoff:3.500A)
      removed outlier: 5.746A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 14
      removed outlier: 6.927A  pdb=" N   VAL L  34 " --> pdb=" O   TYR L  50 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   TYR L  50 " --> pdb=" O   VAL L  34 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120
      removed outlier: 6.189A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 147
      removed outlier: 3.877A  pdb=" N   ALA L 195 " --> pdb=" O   LYS L 151 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 146 through 147
    Processing sheet with id=AB4, first strand: chain 'R' and resid 381 through 383

    381 hydrogen bonds defined for protein.
    1065 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.52

  Time building geometry restraints manager: 3.38 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.34: 2228
        1.34 -     1.46: 2136
        1.46 -     1.59: 3373
        1.59 -     1.71: 0
        1.71 -     1.83: 44
  Bond restraints: 7781
  Sorted by residual:
  bond pdb=" CB  TRP H 102 "
       pdb=" CG  TRP H 102 "
    ideal  model  delta    sigma   weight residual
    1.498  1.420  0.078 3.10e-02 1.04e+03 6.30e+00
  bond pdb=" C   VAL R 459 "
       pdb=" N   PRO R 460 "
    ideal  model  delta    sigma   weight residual
    1.335  1.369 -0.034 1.36e-02 5.41e+03 6.12e+00
  bond pdb=" CB  TRP R 242 "
       pdb=" CG  TRP R 242 "
    ideal  model  delta    sigma   weight residual
    1.498  1.427  0.071 3.10e-02 1.04e+03 5.30e+00
  bond pdb=" CB  PHE H 180 "
       pdb=" CG  PHE H 180 "
    ideal  model  delta    sigma   weight residual
    1.502  1.454  0.048 2.30e-02 1.89e+03 4.36e+00
  bond pdb=" CB  VAL R 215 "
       pdb=" CG2 VAL R 215 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.31e+00
  ... (remaining 7776 not shown)

  Histogram of bond angle deviations from ideal:
       98.63 -   105.72: 151
      105.72 -   112.81: 4086
      112.81 -   119.90: 2701
      119.90 -   126.98: 3534
      126.98 -   134.07: 118
  Bond angle restraints: 10590
  Sorted by residual:
  angle pdb=" C   GLU R 202 "
        pdb=" N   SER R 203 "
        pdb=" CA  SER R 203 "
      ideal   model   delta    sigma   weight residual
     121.54  130.77   -9.23 1.91e+00 2.74e-01 2.33e+01
  angle pdb=" C   PHE R 196 "
        pdb=" N   VAL R 197 "
        pdb=" CA  VAL R 197 "
      ideal   model   delta    sigma   weight residual
     122.13  129.76   -7.63 1.85e+00 2.92e-01 1.70e+01
  angle pdb=" C   MET R 261 "
        pdb=" N   GLU R 262 "
        pdb=" CA  GLU R 262 "
      ideal   model   delta    sigma   weight residual
     121.54  128.99   -7.45 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" C   ALA R1048 "
        pdb=" N   THR R1049 "
        pdb=" CA  THR R1049 "
      ideal   model   delta    sigma   weight residual
     121.70  128.66   -6.96 1.80e+00 3.09e-01 1.50e+01
  angle pdb=" C   SER H 217 "
        pdb=" N   ASN H 218 "
        pdb=" CA  ASN H 218 "
      ideal   model   delta    sigma   weight residual
     121.54  128.92   -7.38 1.91e+00 2.74e-01 1.49e+01
  ... (remaining 10585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4139
       17.84 -    35.67: 352
       35.67 -    53.51: 65
       53.51 -    71.35: 9
       71.35 -    89.18: 7
  Dihedral angle restraints: 4572
    sinusoidal: 1720
      harmonic: 2852
  Sorted by residual:
  dihedral pdb=" CA  PRO H 199 "
           pdb=" C   PRO H 199 "
           pdb=" N   SER H 200 "
           pdb=" CA  SER H 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.94   23.06     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  THR R 252 "
           pdb=" C   THR R 252 "
           pdb=" N   THR R 253 "
           pdb=" CA  THR R 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.35  -22.65     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  ASN R 217 "
           pdb=" C   ASN R 217 "
           pdb=" N   CYS R 218 "
           pdb=" CA  CYS R 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.48   21.52     0      5.00e+00 4.00e-02 1.85e+01
  ... (remaining 4569 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 722
       0.046 -    0.092: 305
       0.092 -    0.137: 115
       0.137 -    0.183: 35
       0.183 -    0.229: 13
  Chirality restraints: 1190
  Sorted by residual:
  chirality pdb=" CB  VAL R 197 "
            pdb=" CA  VAL R 197 "
            pdb=" CG1 VAL R 197 "
            pdb=" CG2 VAL R 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CG  LEU H  89 "
            pdb=" CB  LEU H  89 "
            pdb=" CD1 LEU H  89 "
            pdb=" CD2 LEU H  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CB  ILE K  98 "
            pdb=" CA  ILE K  98 "
            pdb=" CG1 ILE K  98 "
            pdb=" CG2 ILE K  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 1187 not shown)

  Planarity restraints: 1334
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H 215 "   -0.046 5.00e-02 4.00e+02   6.81e-02 7.42e+00
        pdb=" N   PRO H 216 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO H 216 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H 216 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU R 194 "   -0.042 5.00e-02 4.00e+02   6.37e-02 6.48e+00
        pdb=" N   PRO R 195 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO R 195 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 195 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R 238 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   TRP R 238 "    0.043 2.00e-02 2.50e+03
        pdb=" O   TRP R 238 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ILE R 239 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1331 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1672
        2.77 -     3.30: 7298
        3.30 -     3.84: 12541
        3.84 -     4.37: 13931
        4.37 -     4.90: 23896
  Nonbonded interactions: 59338
  Sorted by model distance:
  nonbonded pdb=" O   GLN K   3 "
            pdb=" OG  SER K  25 "
     model   vdw
     2.240 2.440
  nonbonded pdb=" O   VAL R 513 "
            pdb=" OG1 THR R 516 "
     model   vdw
     2.258 2.440
  nonbonded pdb=" O   TYR L 188 "
            pdb=" OH  TYR L 194 "
     model   vdw
     2.261 2.440
  nonbonded pdb=" O   SER H 142 "
            pdb=" OG  SER H 146 "
     model   vdw
     2.272 2.440
  nonbonded pdb=" OE1 GLU R 308 "
            pdb=" OG  SER R 379 "
     model   vdw
     2.281 2.440
  ... (remaining 59333 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4857      2.51       5
     N    1273      2.21       5
     O    1432      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          7.320
  Check model and map are aligned:         0.120
  Convert atoms to be neutral:             0.060
  Process input model:                     24.570
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.010   0.088   7781  Z= 0.636
  Angle     :  1.077  10.309  10590  Z= 0.590
  Chirality :  0.062   0.229   1190
  Planarity :  0.008   0.068   1334
  Dihedral  : 14.271  89.182   2723
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.31 %
    Favored  : 89.59 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.26), residues: 970
  helix: -1.13 (0.26), residues: 312
  sheet: -0.83 (0.34), residues: 238
  loop : -2.25 (0.29), residues: 420

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1903
  time to fit residues: 18.8059
Evaluate side-chains
  47 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 1.126 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.2149
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0010
   chunk 25 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0170
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.5626

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
L   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.077   7781  Z= 0.177
  Angle     :  0.645   9.027  10590  Z= 0.341
  Chirality :  0.043   0.189   1190
  Planarity :  0.005   0.059   1334
  Dihedral  :  5.777  25.569   1067
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer Outliers :  0.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.27), residues: 970
  helix: -0.26 (0.28), residues: 320
  sheet: -0.76 (0.33), residues: 240
  loop : -2.07 (0.31), residues: 410

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 64
  average time/residue: 0.1885
  time to fit residues: 17.4463
Evaluate side-chains
  56 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.857 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0631
  time to fit residues: 1.4957
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 73 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 88 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 87 optimal weight:    0.0050
   chunk 30 optimal weight:    0.6980
   chunk 70 optimal weight:    8.9990
   overall best weight:    1.8798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.085   7781  Z= 0.272
  Angle     :  0.648   8.091  10590  Z= 0.342
  Chirality :  0.042   0.154   1190
  Planarity :  0.004   0.044   1334
  Dihedral  :  5.546  27.383   1067
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.18 %
    Favored  : 90.82 %
  Rotamer Outliers :  0.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.27), residues: 970
  helix:  0.02 (0.29), residues: 320
  sheet: -0.71 (0.33), residues: 247
  loop : -2.03 (0.31), residues: 403

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 59
  average time/residue: 0.1574
  time to fit residues: 14.2340
Evaluate side-chains
  58 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.892 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0704
  time to fit residues: 1.4843
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    0.0270
   chunk 66 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0970
   chunk 9 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 93 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 83 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4636

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.095   7781  Z= 0.151
  Angle     :  0.574   6.942  10590  Z= 0.300
  Chirality :  0.041   0.154   1190
  Planarity :  0.004   0.080   1334
  Dihedral  :  4.989  26.797   1067
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer Outliers :  0.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.27), residues: 970
  helix:  0.33 (0.29), residues: 320
  sheet: -0.56 (0.33), residues: 247
  loop : -1.94 (0.31), residues: 403

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.911 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 65
  average time/residue: 0.1600
  time to fit residues: 15.7138
Evaluate side-chains
  57 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.917 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0658
  time to fit residues: 1.2990
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 1 optimal weight:    0.1980
   chunk 69 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 23 optimal weight:    8.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
L   4 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.137   7781  Z= 0.235
  Angle     :  0.613  10.788  10590  Z= 0.320
  Chirality :  0.041   0.159   1190
  Planarity :  0.005   0.101   1334
  Dihedral  :  4.884  26.804   1067
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer Outliers :  0.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.27), residues: 970
  helix:  0.42 (0.29), residues: 321
  sheet: -0.48 (0.33), residues: 247
  loop : -1.89 (0.32), residues: 402

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 6
  residues processed: 61
  average time/residue: 0.1619
  time to fit residues: 14.7974
Evaluate side-chains
  61 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.953 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0810
  time to fit residues: 2.1322
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0980
   chunk 23 optimal weight:    8.9990
   chunk 93 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7781  Z= 0.168
  Angle     :  0.583   8.092  10590  Z= 0.301
  Chirality :  0.041   0.173   1190
  Planarity :  0.004   0.074   1334
  Dihedral  :  4.717  25.948   1067
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer Outliers :  0.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.28), residues: 970
  helix:  0.47 (0.29), residues: 322
  sheet: -0.38 (0.34), residues: 247
  loop : -1.82 (0.32), residues: 401

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 4
  residues processed: 66
  average time/residue: 0.1527
  time to fit residues: 15.6780
Evaluate side-chains
  56 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 1.016 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0700
  time to fit residues: 1.8049
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7781  Z= 0.198
  Angle     :  0.599   6.920  10590  Z= 0.308
  Chirality :  0.041   0.154   1190
  Planarity :  0.004   0.060   1334
  Dihedral  :  4.721  25.295   1067
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer Outliers :  0.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.28), residues: 970
  helix:  0.63 (0.30), residues: 315
  sheet: -0.35 (0.34), residues: 249
  loop : -1.75 (0.32), residues: 406

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 60
  average time/residue: 0.1530
  time to fit residues: 14.3346
Evaluate side-chains
  55 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.938 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0737
  time to fit residues: 1.6432
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 55 optimal weight:    0.0040
   chunk 28 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 8 optimal weight:    0.0020
   chunk 73 optimal weight:    3.9990
   chunk 85 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   chunk 81 optimal weight:    7.9990
   overall best weight:    1.4006

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7781  Z= 0.218
  Angle     :  0.617   6.784  10590  Z= 0.317
  Chirality :  0.042   0.162   1190
  Planarity :  0.004   0.055   1334
  Dihedral  :  4.776  24.648   1067
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer Outliers :  0.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.28), residues: 970
  helix:  0.63 (0.30), residues: 316
  sheet: -0.25 (0.35), residues: 241
  loop : -1.78 (0.32), residues: 413

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.966 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 1
  residues processed: 58
  average time/residue: 0.1600
  time to fit residues: 14.4479
Evaluate side-chains
  55 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.966 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0711
  time to fit residues: 1.3926
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 89 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 82 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 57 optimal weight:    6.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7781  Z= 0.279
  Angle     :  0.649   7.008  10590  Z= 0.336
  Chirality :  0.042   0.162   1190
  Planarity :  0.004   0.047   1334
  Dihedral  :  4.959  24.746   1067
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer Outliers :  0.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.28), residues: 970
  helix:  0.68 (0.30), residues: 314
  sheet: -0.29 (0.35), residues: 243
  loop : -1.82 (0.32), residues: 413

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.993 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 59
  average time/residue: 0.1558
  time to fit residues: 14.1856
Evaluate side-chains
  52 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.977 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0673
  time to fit residues: 1.3452
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 96 optimal weight:    7.9990
   chunk 88 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    2.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7781  Z= 0.342
  Angle     :  0.705  10.079  10590  Z= 0.367
  Chirality :  0.044   0.165   1190
  Planarity :  0.004   0.046   1334
  Dihedral  :  5.116  25.050   1067
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  8.56 %
    Favored  : 91.34 %
  Rotamer Outliers :  0.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.28), residues: 970
  helix:  0.57 (0.29), residues: 314
  sheet: -0.28 (0.35), residues: 239
  loop : -1.90 (0.31), residues: 417

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.979 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 48
  average time/residue: 0.1653
  time to fit residues: 12.5027
Evaluate side-chains
  49 residues out of total 828 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 48
  time to evaluate  : 0.964 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0826
  time to fit residues: 1.4374
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0970
   chunk 79 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** L   4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.074443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.059281 restraints weight = 33740.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.060829 restraints weight = 19196.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.061809 restraints weight = 13367.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7781  Z= 0.171
  Angle     :  0.617   8.173  10590  Z= 0.314
  Chirality :  0.042   0.151   1190
  Planarity :  0.004   0.045   1334
  Dihedral  :  4.701  22.300   1067
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.70 %
    Favored  : 93.20 %
  Rotamer Outliers :  0.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.28), residues: 970
  helix:  0.80 (0.30), residues: 313
  sheet: -0.17 (0.35), residues: 238
  loop : -1.82 (0.31), residues: 419

===============================================================================
Job complete
usr+sys time: 1424.74 seconds
wall clock time: 26 minutes 48.58 seconds (1608.58 seconds total)